Starting phenix.real_space_refine on Thu Jul 24 22:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.map" model { file = "/net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnk_34167/07_2025/8gnk_34167.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 4100 2.51 5 N 940 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4177 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 23, 'TRANS': 501} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Unusual residues: {' CL': 1, ' NA': 1, 'ABU': 1, 'CLR': 6, 'NAG': 2, 'PTY': 1} Classifications: {'undetermined': 12, 'water': 6} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.40, per 1000 atoms: 1.04 Number of scatterers: 6164 At special positions: 0 Unit cell: (79.776, 85.593, 110.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 43 16.00 P 1 15.00 Na 1 11.00 O 1078 8.00 N 940 7.00 C 4100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 184 " " NAG A 602 " - " ASN A 176 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 960.0 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 57.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.889A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 111 through 118 removed outlier: 4.159A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 118 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 4.094A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.878A pdb=" N THR A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.866A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.815A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 281 through 297 removed outlier: 4.034A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.833A pdb=" N ALA A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 350 removed outlier: 3.740A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.919A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.590A pdb=" N LEU A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 436 Processing helix chain 'A' and resid 437 through 440 removed outlier: 4.020A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.906A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 503 through 519 removed outlier: 3.532A pdb=" N MET A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.956A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.849A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.886A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.762A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.539A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA2, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.512A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.528A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.630A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.844A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 905 1.32 - 1.45: 1892 1.45 - 1.57: 3479 1.57 - 1.70: 2 1.70 - 1.82: 68 Bond restraints: 6346 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CA SER A 378 " pdb=" CB SER A 378 " ideal model delta sigma weight residual 1.534 1.492 0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LYS A 448 " pdb=" O LYS A 448 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.26e-02 6.30e+03 1.08e+01 bond pdb=" C PRO A 376 " pdb=" O PRO A 376 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" CA LYS A 76 " pdb=" C LYS A 76 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.27e-02 6.20e+03 9.60e+00 ... (remaining 6341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 8404 1.76 - 3.52: 193 3.52 - 5.27: 36 5.27 - 7.03: 13 7.03 - 8.79: 3 Bond angle restraints: 8649 Sorted by residual: angle pdb=" N ASN A 66 " pdb=" CA ASN A 66 " pdb=" C ASN A 66 " ideal model delta sigma weight residual 113.43 106.23 7.20 1.26e+00 6.30e-01 3.27e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 113.78 104.99 8.79 1.62e+00 3.81e-01 2.94e+01 angle pdb=" N SER A 295 " pdb=" CA SER A 295 " pdb=" C SER A 295 " ideal model delta sigma weight residual 112.45 106.28 6.17 1.39e+00 5.18e-01 1.97e+01 angle pdb=" N LEU A 64 " pdb=" CA LEU A 64 " pdb=" C LEU A 64 " ideal model delta sigma weight residual 113.21 108.41 4.80 1.15e+00 7.56e-01 1.74e+01 angle pdb=" N LYS A 117 " pdb=" CA LYS A 117 " pdb=" C LYS A 117 " ideal model delta sigma weight residual 113.23 108.11 5.12 1.24e+00 6.50e-01 1.70e+01 ... (remaining 8644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 3615 23.10 - 46.21: 294 46.21 - 69.31: 37 69.31 - 92.41: 1 92.41 - 115.52: 3 Dihedral angle restraints: 3950 sinusoidal: 1793 harmonic: 2157 Sorted by residual: dihedral pdb=" N CYS A 173 " pdb=" C CYS A 173 " pdb=" CA CYS A 173 " pdb=" CB CYS A 173 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C CYS A 173 " pdb=" N CYS A 173 " pdb=" CA CYS A 173 " pdb=" CB CYS A 173 " ideal model delta harmonic sigma weight residual -122.60 -134.45 11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -50.38 -35.62 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 899 0.085 - 0.169: 59 0.169 - 0.254: 4 0.254 - 0.338: 1 0.338 - 0.423: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA CYS A 173 " pdb=" N CYS A 173 " pdb=" C CYS A 173 " pdb=" CB CYS A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ASN A 66 " pdb=" N ASN A 66 " pdb=" C ASN A 66 " pdb=" CB ASN A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 961 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 162 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C LYS A 162 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS A 162 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 163 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 57 " 0.010 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C CYS A 57 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS A 57 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 58 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 95 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO L 96 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.030 5.00e-02 4.00e+02 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1435 2.78 - 3.31: 5596 3.31 - 3.84: 10011 3.84 - 4.37: 11968 4.37 - 4.90: 21040 Nonbonded interactions: 50050 Sorted by model distance: nonbonded pdb=" OH TYR L 95 " pdb=" OE2 GLU H 50 " model vdw 2.252 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.258 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.288 3.040 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR A 523 " pdb=" O TYR A 527 " model vdw 2.310 3.040 ... (remaining 50045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6351 Z= 0.261 Angle : 0.671 8.791 8661 Z= 0.414 Chirality : 0.046 0.423 964 Planarity : 0.004 0.053 1021 Dihedral : 15.250 115.518 2575 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.47 % Allowed : 23.82 % Favored : 75.71 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 745 helix: 0.97 (0.28), residues: 374 sheet: 0.49 (0.56), residues: 108 loop : -0.85 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.001 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.016 0.001 TYR A 554 ARG 0.008 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 1.16722 ( 6) hydrogen bonds : bond 0.21018 ( 322) hydrogen bonds : angle 7.03133 ( 921) SS BOND : bond 0.01011 ( 3) SS BOND : angle 1.24291 ( 6) covalent geometry : bond 0.00415 ( 6346) covalent geometry : angle 0.66959 ( 8649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.696 Fit side-chains REVERT: A 318 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7654 (ttt-90) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.2458 time to fit residues: 24.7950 Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104465 restraints weight = 7233.123| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.26 r_work: 0.2747 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6351 Z= 0.122 Angle : 0.526 9.535 8661 Z= 0.267 Chirality : 0.040 0.168 964 Planarity : 0.004 0.053 1021 Dihedral : 8.446 90.559 1299 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.52 % Allowed : 22.40 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.32), residues: 745 helix: 1.56 (0.27), residues: 375 sheet: 0.56 (0.56), residues: 108 loop : -0.68 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.001 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.011 0.001 TYR L 95 ARG 0.003 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 2) link_NAG-ASN : angle 1.98034 ( 6) hydrogen bonds : bond 0.04459 ( 322) hydrogen bonds : angle 4.73596 ( 921) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.07892 ( 6) covalent geometry : bond 0.00276 ( 6346) covalent geometry : angle 0.52277 ( 8649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.784 Fit side-chains REVERT: A 183 THR cc_start: 0.6902 (OUTLIER) cc_final: 0.6376 (t) REVERT: A 227 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7085 (t80) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.2016 time to fit residues: 23.8413 Evaluate side-chains 84 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101863 restraints weight = 7309.333| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.26 r_work: 0.2706 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6351 Z= 0.161 Angle : 0.548 11.079 8661 Z= 0.276 Chirality : 0.041 0.165 964 Planarity : 0.004 0.053 1021 Dihedral : 7.952 73.204 1296 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.94 % Allowed : 21.92 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 745 helix: 1.64 (0.27), residues: 377 sheet: 0.39 (0.55), residues: 107 loop : -0.79 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 230 HIS 0.003 0.001 HIS H 80 PHE 0.016 0.002 PHE A 339 TYR 0.013 0.001 TYR L 95 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 2) link_NAG-ASN : angle 2.56311 ( 6) hydrogen bonds : bond 0.04650 ( 322) hydrogen bonds : angle 4.49098 ( 921) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.00585 ( 6) covalent geometry : bond 0.00391 ( 6346) covalent geometry : angle 0.54362 ( 8649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.731 Fit side-chains REVERT: A 227 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7048 (t80) outliers start: 25 outliers final: 19 residues processed: 97 average time/residue: 0.2034 time to fit residues: 26.0498 Evaluate side-chains 96 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 4 optimal weight: 0.0070 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.092185 restraints weight = 7501.532| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.36 r_work: 0.2999 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6351 Z= 0.094 Angle : 0.484 9.366 8661 Z= 0.240 Chirality : 0.038 0.154 964 Planarity : 0.004 0.053 1021 Dihedral : 6.769 58.480 1296 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.00 % Allowed : 23.82 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.32), residues: 745 helix: 2.05 (0.27), residues: 376 sheet: 0.40 (0.55), residues: 107 loop : -0.67 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.009 0.001 PHE A 255 TYR 0.008 0.001 TYR A 139 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 4.34315 ( 6) hydrogen bonds : bond 0.03488 ( 322) hydrogen bonds : angle 4.16207 ( 921) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.58071 ( 6) covalent geometry : bond 0.00205 ( 6346) covalent geometry : angle 0.47035 ( 8649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.640 Fit side-chains REVERT: A 183 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6687 (p) REVERT: A 227 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 566 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7208 (tpp80) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.2056 time to fit residues: 26.0025 Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105069 restraints weight = 7333.166| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.32 r_work: 0.2715 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6351 Z= 0.140 Angle : 0.510 6.564 8661 Z= 0.259 Chirality : 0.039 0.161 964 Planarity : 0.004 0.051 1021 Dihedral : 6.879 58.159 1296 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.10 % Allowed : 22.56 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.32), residues: 745 helix: 2.00 (0.27), residues: 376 sheet: 0.29 (0.55), residues: 107 loop : -0.81 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.002 0.001 HIS H 80 PHE 0.016 0.002 PHE A 339 TYR 0.015 0.001 TYR L 95 ARG 0.004 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 2) link_NAG-ASN : angle 3.68168 ( 6) hydrogen bonds : bond 0.04148 ( 322) hydrogen bonds : angle 4.20847 ( 921) SS BOND : bond 0.00381 ( 3) SS BOND : angle 0.83813 ( 6) covalent geometry : bond 0.00337 ( 6346) covalent geometry : angle 0.50022 ( 8649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.711 Fit side-chains REVERT: A 172 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7136 (mtt180) REVERT: A 183 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6295 (p) REVERT: A 227 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7086 (t80) REVERT: H 89 GLU cc_start: 0.8268 (mp0) cc_final: 0.7998 (mp0) outliers start: 26 outliers final: 19 residues processed: 99 average time/residue: 0.2028 time to fit residues: 26.5205 Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105856 restraints weight = 7240.664| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.29 r_work: 0.2725 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6351 Z= 0.129 Angle : 0.491 5.722 8661 Z= 0.250 Chirality : 0.039 0.158 964 Planarity : 0.004 0.054 1021 Dihedral : 6.762 59.745 1296 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.89 % Allowed : 21.92 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.32), residues: 745 helix: 2.05 (0.27), residues: 377 sheet: 0.27 (0.55), residues: 107 loop : -0.80 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.002 0.001 HIS H 80 PHE 0.013 0.001 PHE A 339 TYR 0.016 0.001 TYR L 95 ARG 0.006 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 3.11848 ( 6) hydrogen bonds : bond 0.03944 ( 322) hydrogen bonds : angle 4.16594 ( 921) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.98727 ( 6) covalent geometry : bond 0.00309 ( 6346) covalent geometry : angle 0.48369 ( 8649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.723 Fit side-chains REVERT: A 172 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7111 (mtp180) REVERT: A 183 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6305 (p) REVERT: A 227 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7016 (t80) REVERT: L 92 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: H 89 GLU cc_start: 0.8265 (mp0) cc_final: 0.7995 (mp0) outliers start: 31 outliers final: 21 residues processed: 100 average time/residue: 0.1979 time to fit residues: 26.1631 Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106996 restraints weight = 7307.273| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.31 r_work: 0.2757 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6351 Z= 0.111 Angle : 0.479 5.696 8661 Z= 0.244 Chirality : 0.038 0.155 964 Planarity : 0.004 0.051 1021 Dihedral : 6.558 58.578 1296 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.10 % Allowed : 23.03 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 745 helix: 2.14 (0.27), residues: 377 sheet: 0.32 (0.55), residues: 107 loop : -0.74 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.015 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 2.80715 ( 6) hydrogen bonds : bond 0.03697 ( 322) hydrogen bonds : angle 4.09644 ( 921) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.39891 ( 6) covalent geometry : bond 0.00260 ( 6346) covalent geometry : angle 0.47263 ( 8649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.688 Fit side-chains REVERT: A 172 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7462 (mtp180) REVERT: A 183 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6278 (p) REVERT: A 227 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7057 (t80) REVERT: L 92 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: H 89 GLU cc_start: 0.8216 (mp0) cc_final: 0.7905 (mp0) outliers start: 26 outliers final: 17 residues processed: 100 average time/residue: 0.2020 time to fit residues: 26.6434 Evaluate side-chains 97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.0570 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106226 restraints weight = 7213.332| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.29 r_work: 0.2740 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6351 Z= 0.126 Angle : 0.490 5.708 8661 Z= 0.250 Chirality : 0.039 0.157 964 Planarity : 0.004 0.055 1021 Dihedral : 6.474 58.924 1296 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.26 % Allowed : 23.03 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.32), residues: 745 helix: 2.14 (0.27), residues: 377 sheet: 0.33 (0.55), residues: 107 loop : -0.72 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.014 0.001 PHE A 339 TYR 0.016 0.001 TYR L 95 ARG 0.006 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 2) link_NAG-ASN : angle 2.56025 ( 6) hydrogen bonds : bond 0.03878 ( 322) hydrogen bonds : angle 4.11639 ( 921) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.48755 ( 6) covalent geometry : bond 0.00302 ( 6346) covalent geometry : angle 0.48453 ( 8649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.672 Fit side-chains REVERT: A 183 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6471 (p) REVERT: A 227 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7048 (t80) REVERT: L 92 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: H 89 GLU cc_start: 0.8228 (mp0) cc_final: 0.7904 (mp0) outliers start: 27 outliers final: 20 residues processed: 97 average time/residue: 0.1938 time to fit residues: 24.7905 Evaluate side-chains 97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.090802 restraints weight = 7438.832| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.32 r_work: 0.2930 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6351 Z= 0.131 Angle : 0.494 5.719 8661 Z= 0.251 Chirality : 0.039 0.158 964 Planarity : 0.004 0.053 1021 Dihedral : 6.426 57.006 1296 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.42 % Allowed : 22.71 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.32), residues: 745 helix: 2.13 (0.27), residues: 377 sheet: 0.35 (0.55), residues: 107 loop : -0.72 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.014 0.001 PHE A 339 TYR 0.016 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 2) link_NAG-ASN : angle 2.38886 ( 6) hydrogen bonds : bond 0.03919 ( 322) hydrogen bonds : angle 4.12737 ( 921) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.30822 ( 6) covalent geometry : bond 0.00315 ( 6346) covalent geometry : angle 0.48956 ( 8649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.648 Fit side-chains REVERT: A 172 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7611 (mtt180) REVERT: A 183 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6472 (p) REVERT: A 227 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7220 (t80) REVERT: L 92 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: H 89 GLU cc_start: 0.8297 (mp0) cc_final: 0.8015 (mp0) outliers start: 28 outliers final: 23 residues processed: 100 average time/residue: 0.1914 time to fit residues: 25.3456 Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107152 restraints weight = 7341.501| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.26 r_work: 0.2790 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6351 Z= 0.095 Angle : 0.462 5.872 8661 Z= 0.234 Chirality : 0.038 0.154 964 Planarity : 0.004 0.054 1021 Dihedral : 6.074 57.959 1296 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.84 % Allowed : 24.29 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.32), residues: 745 helix: 2.32 (0.27), residues: 377 sheet: 0.25 (0.54), residues: 107 loop : -0.66 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.010 0.001 PHE A 51 TYR 0.012 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 2) link_NAG-ASN : angle 2.17360 ( 6) hydrogen bonds : bond 0.03332 ( 322) hydrogen bonds : angle 3.99856 ( 921) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.93993 ( 6) covalent geometry : bond 0.00212 ( 6346) covalent geometry : angle 0.45812 ( 8649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.649 Fit side-chains REVERT: A 172 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7485 (mtt180) REVERT: A 183 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6438 (p) REVERT: A 227 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 281 ASP cc_start: 0.8430 (t0) cc_final: 0.8169 (t0) REVERT: H 89 GLU cc_start: 0.8199 (mp0) cc_final: 0.7877 (mp0) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1994 time to fit residues: 24.7338 Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.142972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104763 restraints weight = 7409.681| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.27 r_work: 0.2754 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6351 Z= 0.121 Angle : 0.486 6.433 8661 Z= 0.245 Chirality : 0.038 0.157 964 Planarity : 0.004 0.053 1021 Dihedral : 6.138 56.583 1296 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.31 % Allowed : 23.82 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.32), residues: 745 helix: 2.25 (0.27), residues: 378 sheet: 0.17 (0.54), residues: 107 loop : -0.67 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.013 0.001 PHE A 339 TYR 0.017 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 2) link_NAG-ASN : angle 2.15881 ( 6) hydrogen bonds : bond 0.03719 ( 322) hydrogen bonds : angle 4.04150 ( 921) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.15563 ( 6) covalent geometry : bond 0.00289 ( 6346) covalent geometry : angle 0.48165 ( 8649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3751.29 seconds wall clock time: 65 minutes 4.01 seconds (3904.01 seconds total)